Biomarkers include genetic and epigenetic markers, such as mutations, deletions, insertions, rearrangements, and polymorphisms, including single nucleotide polymorphisms (SNP), copy number variations, biallelic polymorphisms, including multinucleotide changes, repeats, translocations, and epigenetic changes such as gene hypermethylation. Variations, including DNA mutations, can occur as the result of inherited (inborn) genetic errors or as acquired (somatic) mutations, resulting, for example, from environmental insults and the process of aging or disease process. For example, mutations in oncogenes and tumor suppressor genes can contribute to the predisposition, incidence, and progression of cancer. Thus, genetic and epigenetic variations can be markers of diseases or conditions. Available methods and assay systems for detecting and analyzing various biomarkers and for screening and diagnosis of cancer and other diseases and conditions, have not been entirely satisfactory. Methods and assay systems are needed for detecting and analyzing various biomarkers for screening, detecting, and diagnosing diseases and conditions, such as cancer, and monitoring corresponding therapeutic intervention, such as chemotherapy.